GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids
Journal article, 2022

Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa or indications of horizontal gene transfer events. While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. GEnView (Genetic Environment View) is a Python-based pipeline for the comparative analysis of gene-loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to the >800.000 genomes and plasmids currently available in the NCBI Assembly and RefSeq databases, and is able to process local genomes that are not deposited at NCBI, enabling searches for genomic sequences and to analyze their genetic environments through the interactive visualization and extensive metadata files created by GEnView.

Author

Stefan Ebmeyer

University of Gothenburg

Roelof Dirk Coertze

University of Gothenburg

Fanny Berglund

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

University of Gothenburg

Erik Kristiansson

Chalmers, Mathematical Sciences, Applied Mathematics and Statistics

University of Gothenburg

D. G. Joakim Larsson

University of Gothenburg

Bioinformatics

1367-4803 (ISSN) 13674811 (eISSN)

Vol. 38 6 1727-1728

Subject Categories

Bioinformatics and Systems Biology

Genetics

DOI

10.1093/bioinformatics/btab855

PubMed

34951622

More information

Latest update

5/30/2022